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- PDB-3wi6: Crystal structure of MAPKAP Kinase-2 (MK2) in complex with non-se... -

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Basic information

Entry
Database: PDB / ID: 3wi6
TitleCrystal structure of MAPKAP Kinase-2 (MK2) in complex with non-selective inhibitor
ComponentsMAP kinase-activated protein kinase 2
KeywordsTransferase/Transferase inhibitor / Gly-rich loop formed / ATP-binding / Kinase / Nucleotide-binding / Phosphoprotein / Serine/threonine-protein kinase / Transferase-Transferase inhibitor complex
Function / homology
Function and homology information


macropinocytosis / CREB phosphorylation / calcium-dependent protein serine/threonine kinase activity / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / leukotriene metabolic process / Synthesis of Leukotrienes (LT) and Eoxins (EX) / regulation of tumor necrosis factor production / regulation of tumor necrosis factor-mediated signaling pathway / calmodulin-dependent protein kinase activity ...macropinocytosis / CREB phosphorylation / calcium-dependent protein serine/threonine kinase activity / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / leukotriene metabolic process / Synthesis of Leukotrienes (LT) and Eoxins (EX) / regulation of tumor necrosis factor production / regulation of tumor necrosis factor-mediated signaling pathway / calmodulin-dependent protein kinase activity / positive regulation of macrophage cytokine production / mitogen-activated protein kinase binding / regulation of interleukin-6 production / 3'-UTR-mediated mRNA stabilization / toll-like receptor signaling pathway / p38MAPK cascade / inner ear development / Regulation of HSF1-mediated heat shock response / cellular response to vascular endothelial growth factor stimulus / vascular endothelial growth factor receptor signaling pathway / regulation of cellular response to heat / p38MAPK events / regulation of mRNA stability / response to cytokine / activated TAK1 mediates p38 MAPK activation / Regulation of TNFR1 signaling / VEGFA-VEGFR2 Pathway / MAPK cascade / positive regulation of tumor necrosis factor production / peptidyl-serine phosphorylation / Oxidative Stress Induced Senescence / response to lipopolysaccharide / calmodulin binding / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / inflammatory response / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / DNA damage response / extracellular exosome / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
MAP kinase activated protein kinase, C-terminal / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site ...MAP kinase activated protein kinase, C-terminal / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-YRZ / MAP kinase-activated protein kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 Å
AuthorsFujino, A. / Fukushima, K. / Kubota, T. / Matsumoto, Y. / Takimoto-Kamimura, M.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2013
Title: Structure of the beta-form of human MK2 in complex with the non-selective kinase inhibitor TEI-L03090
Authors: Fujino, A. / Fukushima, K. / Kubota, T. / Matsumoto, Y. / Takimoto-Kamimura, M.
History
DepositionSep 6, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 18, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MAP kinase-activated protein kinase 2
B: MAP kinase-activated protein kinase 2
C: MAP kinase-activated protein kinase 2
D: MAP kinase-activated protein kinase 2
E: MAP kinase-activated protein kinase 2
F: MAP kinase-activated protein kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)226,67812
Polymers225,1286
Non-polymers1,5506
Water0
1
A: MAP kinase-activated protein kinase 2
B: MAP kinase-activated protein kinase 2
C: MAP kinase-activated protein kinase 2
D: MAP kinase-activated protein kinase 2
E: MAP kinase-activated protein kinase 2
F: MAP kinase-activated protein kinase 2
hetero molecules

A: MAP kinase-activated protein kinase 2
B: MAP kinase-activated protein kinase 2
C: MAP kinase-activated protein kinase 2
D: MAP kinase-activated protein kinase 2
E: MAP kinase-activated protein kinase 2
F: MAP kinase-activated protein kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)453,35624
Polymers450,25612
Non-polymers3,10012
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_545-x,-y-1/2,z1
Buried area35980 Å2
ΔGint-239 kcal/mol
Surface area147680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.061, 179.684, 254.101
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121

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Components

#1: Protein
MAP kinase-activated protein kinase 2 / MAPK-activated protein kinase 2 / MAPKAP kinase 2 / MAPKAP-K2 / MAPKAPK-2 / MK-2 / MK2


Mass: 37521.332 Da / Num. of mol.: 6 / Fragment: UNP residues 41-364
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPKAPK2 / Plasmid: pET22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P49137, non-specific serine/threonine protein kinase
#2: Chemical
ChemComp-YRZ / N-[(3S)-piperidin-3-yl]-7,8-dihydro-6H-pyrazolo[1,5-a]pyrrolo[3,2-e]pyrimidin-5-amine


Mass: 258.322 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C13H18N6

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.56 Å3/Da / Density % sol: 73.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1M Na-Acetate, 1.6M Ammonium Sulphate, 200mM NaCl, 1.4mM Deoxi Big Chap, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 28, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.99→100 Å / Num. obs: 82725 / % possible obs: 99.7 % / Redundancy: 5 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 29.5
Reflection shellResolution: 3→3.11 Å / Redundancy: 5 % / Rmerge(I) obs: 0.434 / Mean I/σ(I) obs: 3.1 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NY3

1ny3


Resolution: 2.99→30 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.887 / SU B: 13.826 / SU ML: 0.265 / Cross valid method: THROUGHOUT / ESU R: 0.546 / ESU R Free: 0.358 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28292 4132 5 %RANDOM
Rwork0.24026 ---
obs0.24241 78593 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 67.368 Å2
Baniso -1Baniso -2Baniso -3
1-1.11 Å20 Å20 Å2
2---1.15 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 2.99→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13439 0 114 0 13553
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.02213853
X-RAY DIFFRACTIONr_bond_other_d0.0060.029537
X-RAY DIFFRACTIONr_angle_refined_deg1.5661.97618737
X-RAY DIFFRACTIONr_angle_other_deg0.929323284
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.42451666
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.74423.929593
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.83152436
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6671584
X-RAY DIFFRACTIONr_chiral_restr0.0790.22091
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02114976
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022698
X-RAY DIFFRACTIONr_mcbond_it1.1811.58460
X-RAY DIFFRACTIONr_mcbond_other0.1541.53376
X-RAY DIFFRACTIONr_mcangle_it2.283213675
X-RAY DIFFRACTIONr_scbond_it2.75835393
X-RAY DIFFRACTIONr_scangle_it4.8234.55062
LS refinement shellResolution: 2.988→3.065 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 246 -
Rwork0.303 5454 -
obs--94.67 %

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